NULISAseqR NULISAseqR logo

NULISAseqR is an R package designed for comprehensive analysis of proteomic data from the NULISAseq platform (Alamar Biosciences). NULISAseq is a high-multiplexed proteomic assay that uses nucleic acid-linked immunosandwich assays to measure hundreds of proteins simultaneously.

Features

  • Data Import: Read and parse NULISAseq XML output files
  • Quality Control: QC metrics and visualizations
  • Normalization: Intra-plate and inter-plate normalization using internal controls
  • Statistical Analysis: Differential abundance testing and outcome modeling
  • Visualization: Heatmaps, PCA plots, volcano plots, and more
  • Reporting: Generate comprehensive automated HTML QC reports with metrics and figures

Installation

System Requirements

  • R version 4.4 or higher
  • Installation time: < 5 minutes

macOS Users

Important: Before installing NULISAseqR on macOS, you need to install Xcode Command Line Tools:

  1. Install Xcode from the App Store (if not already installed)
  2. Open Terminal and run:
sudo xcodebuild -license accept

Windows Users

Important: Before installing NULISAseqR on Windows, you need to install Rtools:

  1. Go to https://cran.r-project.org/bin/windows/Rtools/
  2. Download and install the appropriate Rtools version for your R installation
  3. Follow the installation instructions on the website

Installation Steps 

# 1. Install devtools
if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")

# 2. Install BiocManager for Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

# 3. Install ComplexHeatmap from Bioconductor
BiocManager::install("ComplexHeatmap")

# 4. Install ggalt from CRAN snapshot
install.packages('ggalt', repos = "http://packagemanager.posit.co/cran/2025-08-02")

# 5. Install PCAtools (Alamar fork)
devtools::install_github('Alamar-Biosciences/PCAtools')

# 6. Install NULISAseqR
devtools::install_github('Alamar-Biosciences/NULISAseqR')

Note: If you encounter issues installing packages from source, you may need to restart R (Cmd/Ctrl + Shift + F10 in RStudio) between major installation steps.

Load the package:

Resources

Documentation

  • Function Reference - Complete documentation of all package functions
  • User Guide - Detailed tutorials, workflows, and examples
  • News - Release notes and changelog

Getting Help